GEOSS: Gene Expression Open Source System
GEOSS (formerly known as GeneX Va) is a secure, open source database and analysis package used to archive and analyze expression data from gene chip experiments.
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GEOSS is intended to be a multiuser archive for gene chip data, as well as a friendly, powerful analysis tool for end users. It includes workflow management features for the microarray center, and for the individual research labs. Go to the GEOSS web site for information on how to download the latest version for free.

Gene expression data, and the related meta data can be difficult to manage. For this reason, GEOSS was created to handle large amounts of data from gene chip hybridizations. It also includes information about experiments and protocols - the same data typically captured by a LIMS package. GEOSS is not a LIMS package, but much of the same type of information needs to be captured in order to unambiguously identify experiments, and to facilitate future data analyses. We intend that all normal processes can be handles easily by researchers. The web interface has been carefully crafted to flow well, and to be intuitive. Part of the documentation is a step-by-step guide, complete with screen shots.

In addition to the data archive requirements, a good gene expression package needs analysis tools. We invented the "Analysis Tree" concept. Plugin analytical routines are connected together in a flowchart fashion. The tree is inverted with the root at the top. Each node of the tree is an analysis. Data flows through the tree, and since the tree is graphicallly represented, it is easy to visualize. Clicking on each node gives you the properties for that node. Once you hve the properties for each node (each node representing an analytical script), simply run the tree. All the intermediate data files are saved, as well the the final output files.

Underlying all this technology is a robust security system. Modern data stores need to accomodate privacy and security, as well as the flexibility for groups of researchers to work together. GEOSS has this security. We created a system of groups very much like the Unix group system, although easier to manage. Each user in the system can create as many groups as necessary, and add/remove other users from the groups. Some users are primary investigators (PIs) and they own the data. People working with a PI can create studies and orders on the PIs behalf, but the PI still owns nearly everything. With multiple groups, a PI can run several projects, and keep those projects as separate as necessary. We have also taken great care that the servers used to power GEOSS are secure. We use Fedora Linux, and keep up with all releveant security patches. The servers are on a regular backup schedule as well.

With all of this technology, we still kept GEOSS as easy to install as possible. While our documentation is far from perfect, we do have extensive installation instructions, and we are always prompt in answering email and phone queries. On a typical Fedora server, there are a few Perl modules to install, the R statistical package, and an R library. Apache and Postgres need a few configuration adjustments. The actual GEOSS install consists of un packing the archive, editing a config file with some settings for your server, switching to root and running a make file, then switching back to a normal user and running a second make file. After that you use an included script to create GEOSS user accounts, and you can start using the system.

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